These analyses examine the relationship between expression levels and viral titer for a set of genes that we hypothesize have a relationship with viral infection. The overall strategy is to:

  1. Identify a list of candidate genes based on the literature and previous analyses.
  2. Subset our overall set of transcripts to include only those with an annotation containing the name of the candidate gene in the SwissProt gene name, SwissProt gene function, KEGG pathway, or EggNOG gene orthology annotations.
  3. Manually filter search results to remove non-target inclusions
  4. Remove transcripts with no variation in expression for each comparison (e.g., bursa at transcript-level)
  5. Use a linear mixed effects model to assess the relationship between log(expression) and log(viral titer) for each candidate gene/transcript. The model structure is expression ~ virus shedding group + sex + weight on day 55 + age with the sequencing pool as a random effect. The model is run on the entire set, as well as just on treatment groups I1, I3, I5, and I14.
  6. Correct the p-values for multiple testing using a false discovery rate approach with adjusted p-values (i.e., q-value) cutoff of 0.05. Corrections are used for just the test that incorporates all treatment groups because that is the only one used for filtering.
  7. Plot the results

Summarize results

identifier comparison Overall I1 I3 I5 I14
DN13777_c0_g1 BG 0.0000000 0.0002513 0.0000000 0.0000027 0.0306137
DN1920_c0_g1 BG 0.0000730 0.0422958 0.1784600 0.3893947 0.1915490
DN2085_c0_g2 BG 0.0001528 0.0357238 0.2492628 0.5569071 0.1063798
DN1920_c0_g1_i6 BT 0.0000157 0.0075801 0.9441925 0.7194101 NA
DN2085_c0_g2_i11 BT 0.0000954 0.0082810 0.2463535 0.5446737 0.0458006
DN2085_c0_g2_i16 BT 0.0000620 0.0475667 0.3002699 0.3854840 0.0354787
DN6190_c0_g1_i1 BT 0.0000674 0.1522988 0.9103624 0.4416042 0.4908973
DN100201_c0_g1 IG 0.0008980 0.9729533 0.3054243 0.8940546 NA
DN110170_c0_g1 IG 0.0000781 0.1973438 0.0817695 0.5407885 NA
DN12243_c0_g1 IG 0.0011999 0.8042460 0.8925449 0.0998848 NA
DN12298_c0_g1 IG 0.0000058 0.6845210 0.7210647 0.9251891 NA
DN13002_c0_g1 IG 0.0017131 0.8466315 0.8501122 0.7085877 NA
DN13412_c0_g1 IG 0.0000923 0.0555808 0.5543012 0.2649977 NA
DN13777_c0_g1 IG 0.0000000 0.0012386 0.0006619 0.0000088 NA
DN1500_c0_g1 IG 0.0000000 0.0562272 0.0912992 0.1671535 NA
DN15121_c0_g1 IG 0.0000059 0.4594157 0.7630933 0.1108926 NA
DN15388_c0_g1 IG 0.0003863 0.1013209 0.6492220 0.2211440 NA
DN15488_c0_g1 IG 0.0010747 0.3482318 0.7349010 0.1266472 NA
DN15589_c0_g1 IG 0.0002359 0.8887689 0.5540186 0.6238820 NA
DN161_c0_g1 IG 0.0000430 0.1016657 0.4408942 0.1758913 NA
DN1634_c0_g1 IG 0.0000999 0.0639848 0.5753385 0.6263102 NA
DN164_c3_g1 IG 0.0000000 0.0671255 0.5400867 0.0812287 NA
DN16598_c0_g1 IG 0.0000690 0.1913477 0.5307549 0.7552612 NA
DN17675_c0_g2 IG 0.0002623 0.0556842 0.0753158 0.9218469 NA
DN178217_c0_g1 IG 0.0000609 0.1590754 0.6435340 0.8380455 NA
DN18052_c0_g1 IG 0.0000028 0.0182347 0.9707730 0.5177078 NA
DN186640_c0_g2 IG 0.0015594 0.7285444 0.6579217 0.8620476 NA
DN1920_c0_g1 IG 0.0000003 0.1569991 0.1803017 0.9360567 NA
DN1934_c0_g1 IG 0.0000001 0.1098312 0.6869401 0.8259087 NA
DN20116_c0_g1 IG 0.0003483 0.1246020 0.4350566 0.0237274 NA
DN2085_c0_g2 IG 0.0000002 0.1517111 0.5003230 0.2840268 NA
DN20874_c0_g1 IG 0.0000075 0.0798700 0.3355385 0.3000490 NA
DN24849_c0_g1 IG 0.0012369 0.2546948 0.2569467 0.7508500 NA
DN2578_c0_g1 IG 0.0023673 0.1872581 0.5843666 0.9451245 NA
DN2677_c0_g1 IG 0.0003336 0.2945524 0.5780789 0.3927684 NA
DN28958_c0_g1 IG 0.0001016 0.6291364 0.3322306 0.4043615 NA
DN2932_c0_g1 IG 0.0000000 0.0289218 0.7016428 0.0056760 NA
DN30475_c0_g1 IG 0.0003666 0.4763537 0.9857035 0.2482630 NA
DN3126_c0_g1 IG 0.0026766 0.3404283 0.4766454 0.9525649 NA
DN313_c0_g5 IG 0.0001535 0.4672101 0.8039801 0.2333945 NA
DN3236_c0_g1 IG 0.0000361 0.0319201 0.8349911 0.0563487 NA
DN51353_c2_g1 IG 0.0004732 0.0070518 0.2975667 0.6665458 NA
DN55170_c0_g1 IG 0.0011629 0.1310161 0.1172851 0.0373965 NA
DN5594_c0_g1 IG 0.0000872 0.1609228 0.4136014 0.9054869 NA
DN6170_c0_g1 IG 0.0000001 0.0398252 0.8807531 0.9644744 NA
DN6178_c0_g1 IG 0.0000000 0.0615188 0.5532953 0.6988068 NA
DN6190_c0_g1 IG 0.0000000 0.0451872 0.2803643 0.7680450 NA
DN71517_c0_g1 IG 0.0013588 0.1809965 0.7788305 0.6791549 NA
DN718_c0_g1 IG 0.0000251 0.0523404 0.4674518 0.5576083 NA
DN7889_c0_g1 IG 0.0000830 0.0250129 0.3422876 0.7674065 NA
DN7889_c0_g2 IG 0.0000001 0.1462303 0.5199618 0.8463439 NA
DN7919_c0_g1 IG 0.0005107 0.6721794 0.6806076 0.5478266 NA
DN7951_c0_g1 IG 0.0021581 0.9884517 0.8393762 0.0939009 NA
DN861_c0_g1 IG 0.0000323 0.2765972 0.8187419 0.4467934 NA
DN876_c0_g1 IG 0.0003866 0.0368023 0.2898625 0.0259882 NA
DN9204_c0_g1 IG 0.0005322 0.5735275 0.6287088 0.1250009 NA
DN100201_c0_g1_i1 IT 0.0009932 0.9654666 0.3054243 0.8561331 NA
DN110170_c0_g1_i1 IT 0.0002397 0.2450785 0.0851785 0.5293796 NA
DN12243_c0_g1_i2 IT 0.0008549 0.5674254 0.9202142 0.0938546 NA
DN12298_c0_g1_i2 IT 0.0000122 0.5594214 0.7334767 0.7421475 NA
DN13412_c0_g1_i3 IT 0.0001917 0.0793653 0.5730721 0.5735968 NA
DN1500_c0_g1_i13 IT 0.0000007 0.0443897 0.0985899 0.6247716 NA
DN1500_c0_g1_i23 IT 0.0001881 0.2030202 0.2753503 0.4768397 NA
DN15121_c0_g1_i1 IT 0.0000201 0.1963654 0.6627433 0.0546948 NA
DN161_c0_g1_i6 IT 0.0001716 0.0871023 0.4269234 0.9707047 NA
DN1634_c0_g1_i9 IT 0.0005219 0.0532275 0.6416564 0.7363712 NA
DN164_c3_g1_i7 IT 0.0000561 0.0114707 0.3557603 0.9632579 NA
DN16598_c0_g1_i1 IT 0.0001681 0.1679986 0.5928359 0.8962864 NA
DN17675_c0_g2_i1 IT 0.0003087 0.0447098 0.0768030 0.9965439 NA
DN178217_c0_g1_i1 IT 0.0001110 0.1659547 0.6240510 0.7848042 NA
DN18052_c0_g1_i2 IT 0.0000086 0.0577801 0.6711838 0.5381270 NA
DN1920_c0_g1_i1 IT 0.0002308 0.1755185 0.5712582 0.1546070 NA
DN1920_c0_g1_i11 IT 0.0000002 0.1224572 0.1629301 0.9903640 NA
DN1920_c0_g1_i6 IT 0.0009763 0.2637653 0.0408949 0.9170980 NA
DN1920_c0_g1_i9 IT 0.0000008 0.1792891 0.2258073 0.7768433 NA
DN1934_c0_g1_i11 IT 0.0000004 0.1199015 0.7910376 0.4929921 NA
DN1934_c0_g1_i16 IT 0.0000106 0.1560291 0.7869596 0.3694828 NA
DN1934_c0_g1_i9 IT 0.0001888 0.0053421 0.3137414 0.2173266 NA
DN2085_c0_g2_i1 IT 0.0000005 0.0258093 0.5066906 0.7736778 NA
DN2085_c0_g2_i10 IT 0.0000000 0.1471213 0.6951091 0.3135064 NA
DN2085_c0_g2_i11 IT 0.0000000 0.0762403 0.7380844 0.3330106 NA
DN2085_c0_g2_i12 IT 0.0000003 0.0662251 0.4441305 0.1078980 NA
DN2085_c0_g2_i13 IT 0.0000000 0.2719628 0.8115155 0.8686625 NA
DN2085_c0_g2_i14 IT 0.0000000 0.1341612 0.6011004 0.6028858 NA
DN2085_c0_g2_i15 IT 0.0000001 0.0129263 0.7510882 0.3447572 NA
DN2085_c0_g2_i16 IT 0.0000000 0.0623648 0.6055955 0.3374605 NA
DN2085_c0_g2_i5 IT 0.0000000 0.1239977 0.7712695 0.0353374 NA
DN2085_c0_g2_i6 IT 0.0000299 0.2991633 0.6502590 0.9063409 NA
DN20874_c0_g1_i10 IT 0.0000020 0.0239185 0.6224745 0.2167091 NA
DN20874_c0_g1_i11 IT 0.0000311 0.2433851 0.5540562 0.8095258 NA
DN20874_c0_g1_i8 IT 0.0009702 0.1139299 0.4795470 0.7655639 NA
DN20874_c0_g1_i9 IT 0.0000075 0.0761404 0.5307126 0.2622031 NA
DN22_c0_g1_i12 IT 0.0000003 0.0482336 0.7854073 0.2818506 NA
DN2413_c0_g1_i2 IT 0.0000006 0.0257854 0.8808276 0.1338854 NA
DN2413_c0_g1_i3 IT 0.0001297 0.2556587 0.4347207 0.7171360 NA
DN2413_c0_g1_i5 IT 0.0004118 0.1065545 0.4841017 0.2751612 NA
DN2413_c0_g1_i6 IT 0.0000067 0.0421608 0.9284714 0.2416906 NA
DN2413_c0_g1_i8 IT 0.0000210 0.0501715 0.5901812 0.6376000 NA
DN2578_c0_g1_i3 IT 0.0009106 0.6713801 0.2849262 0.0023348 NA
DN2677_c0_g1_i1 IT 0.0005693 0.1544636 0.7122514 0.9818536 NA
DN2932_c0_g1_i6 IT 0.0000000 0.0281588 0.6990479 0.0073432 NA
DN3089_c0_g1_i6 IT 0.0007255 0.0541290 0.4607794 0.3641355 NA
DN3236_c0_g1_i10 IT 0.0000127 0.0308440 0.8002013 0.2339919 NA
DN51353_c2_g1_i2 IT 0.0004592 0.0078940 0.1516855 0.6665458 NA
DN5594_c0_g1_i10 IT 0.0000539 0.1108950 0.5193373 0.9086314 NA
DN5715_c0_g1_i1 IT 0.0012981 0.2869636 0.3276593 0.3635253 NA
DN6170_c0_g1_i10 IT 0.0000003 0.0353065 0.9411996 0.6481887 NA
DN6170_c0_g1_i3 IT 0.0015649 0.1420526 0.1938090 0.2762727 NA
DN6170_c0_g1_i5 IT 0.0003075 0.0355721 0.4453654 0.3396758 NA
DN6178_c0_g1_i1 IT 0.0000000 0.0479820 0.6270454 0.8629915 NA
DN6190_c0_g1_i1 IT 0.0000000 0.0544985 0.0306379 0.8146949 NA
DN6190_c0_g1_i2 IT 0.0000001 0.0453780 0.8031337 0.7402645 NA
DN6190_c0_g1_i4 IT 0.0000000 0.0788023 0.3435785 0.3769021 NA
DN6305_c0_g1_i8 IT 0.0007613 0.3214703 0.7495151 0.5615444 NA
DN71517_c0_g1_i5 IT 0.0015352 0.2277553 0.7756763 0.5301235 NA
DN718_c0_g1_i1 IT 0.0000578 0.0421128 0.4828885 0.6385922 NA
DN718_c0_g1_i3 IT 0.0000187 0.2313407 0.8060180 0.7601099 NA
DN7889_c0_g1_i1 IT 0.0006440 0.0317513 0.7901639 0.8933404 NA
DN7919_c0_g1_i9 IT 0.0005152 0.3604783 0.7075052 0.7314113 NA
DN861_c0_g1_i1 IT 0.0000221 0.2623874 0.8401699 0.4510389 NA
DN9204_c0_g1_i7 IT 0.0006586 0.4486161 0.6809838 0.1538469 NA

Functions for analyzing and plotting data

Plotting significant results